# # ChangeLog for doc/userguide/userguide.xml # # Generated by Trac 1.4.4 # Jan 9, 2025, 5:24:24 PM Mon, 03 Jul 2017 15:06:31 GMT Frederik Heber [3f6aac] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AtomByNameAction.cpp (added) * src/Actions/SelectionAction/Atoms/AtomByNameAction.def (added) * src/Actions/SelectionAction/Atoms/AtomByNameAction.hpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.cpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.def (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomByName/post/ethane-H5_missing.pdb (added) * tests/regression/Selection/Atoms/AtomByName/pre/ethane.pdb (added) * tests/regression/Selection/Atoms/AtomByName/testsuite-selection-select-atoms-by-name.at (added) * tests/regression/Selection/Atoms/AtomByName/testsuite-selection-unselect-atoms-by-name.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added (Un)selectAtomByName. - Descriptor for AtomByName was already ... Mon, 03 Jul 2017 15:01:38 GMT Frederik Heber [f1cacb] * doc/userguide/userguide.xml (modified) Fixed several small issues with the userguide. - additional ... Thu, 22 Jun 2017 22:28:16 GMT Frederik Heber [310445] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/RandomPerturbationAction.cpp (added) * src/Actions/AtomAction/RandomPerturbationAction.def (added) * src/Actions/AtomAction/RandomPerturbationAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Atoms/RandomPerturbation/post/water.xyz (added) * tests/regression/Atoms/RandomPerturbation/pre/water.xyz (added) * tests/regression/Atoms/RandomPerturbation/testsuite-atoms-random-perturbation.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added RandomPerturbationAction. - this should be when doing ... Wed, 21 Jun 2017 22:02:50 GMT Frederik Heber [78ea3c] * doc/userguide/userguide.xml (modified) * src/Actions/Action.hpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (added) * src/Actions/MoleculeAction/RotateAroundBondAction.def (added) * src/Actions/MoleculeAction/RotateAroundBondAction.hpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.def (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/World.cpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/RotateAroundBond/post/test-195-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-90-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-95-false.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/test.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/test_cycle.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (added) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/regression/Molecules/testsuite-molecules.at (modified) * tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (modified) Merge branch 'Docu_Python_wait' into Candidate_v1.6.1 Conflicts: ... Wed, 21 Jun 2017 21:52:01 GMT Frederik Heber [101d2d] * doc/userguide/userguide.xml (modified) DOCU: Added note on necessity of wait() to Python section. Tue, 20 Jun 2017 19:58:36 GMT Frederik Heber [788dce] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (added) * src/Actions/MoleculeAction/RotateAroundBondAction.def (added) * src/Actions/MoleculeAction/RotateAroundBondAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/RotateAroundBond/post/test-195-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-90-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-95-false.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/test.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added RotateAroundBondAction. - TESTS: added regression test. - ... Mon, 19 Jun 2017 08:24:17 GMT Frederik Heber [836972] * doc/userguide/userguide.xml (modified) * src/Actions/GeometryAction/GeometryRemoveAction.cpp (added) * src/Actions/GeometryAction/GeometryRemoveAction.def (added) * src/Actions/GeometryAction/GeometryRemoveAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Geometry/Remove/post/test.xyz (added) * tests/regression/Geometry/Remove/pre/test.xyz (added) * tests/regression/Geometry/Remove/testsuite-geometry-remove.at (added) * tests/regression/Geometry/testsuite-geometry.at (modified) * tests/regression/Makefile.am (modified) Added GeometryRemoveAction. - TESTS: Also added regression test. Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [1ba51c] * doc/userguide/userguide.xml (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) Updated userguide with lots of notes on using geometry object. Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [987145] * doc/userguide/userguide.xml (modified) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.def (added) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.def (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.def (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.def (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/Python/AllActions/options.dat (modified) Added four GeometryActions to convert atom positions into vectors. ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [48eab8] * doc/userguide/userguide.xml (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/QtGeometryList.cpp (added) * src/UIElements/Views/Qt4/QtGeometryList.hpp (added) Added QtGeometryList to QtMainWindow. - this list shows the name ... Fri, 04 Nov 2016 09:37:48 GMT Frederik Heber [2d1280] * doc/userguide/userguide.xml (modified) * src/Actions/BondAction/BondSetDegreeAction.cpp (added) * src/Actions/BondAction/BondSetDegreeAction.def (added) * src/Actions/BondAction/BondSetDegreeAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Bond/SetDegree/post/test.pdb (added) * tests/regression/Bond/SetDegree/post/test_degree1.pdb (added) * tests/regression/Bond/SetDegree/post/test_degree2.pdb (added) * tests/regression/Bond/SetDegree/post/test_multiple.pdb (added) * tests/regression/Bond/SetDegree/post/test_multiple_degree1.pdb (added) * tests/regression/Bond/SetDegree/post/test_multiple_degree2.pdb (added) * tests/regression/Bond/SetDegree/pre/.pdb (added) * tests/regression/Bond/SetDegree/pre/test.pdb (added) * tests/regression/Bond/SetDegree/pre/test_multiple.pdb (added) * tests/regression/Bond/SetDegree/pre/test_multiple_fail.pdb (added) * tests/regression/Bond/SetDegree/testsuite-bond-set-degree.at (added) * tests/regression/Bond/SetDegree/testsuite-bond-set-degree_multiple.at (added) * tests/regression/Bond/testsuite-bond.at (modified) * tests/regression/Makefile.am (modified) Added BondSetDegreeAction for manipulating bond degrees. Thu, 20 Oct 2016 20:54:48 GMT Frederik Heber [72e40d0] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.cpp (added) * src/Actions/WorldAction/StepWorldTimeAction.def (added) * src/Actions/WorldAction/StepWorldTimeAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/testsuite-options.at (modified) * tests/regression/WorldTime/SetWorldTime/testsuite-worldtime-set-world-time.at (moved) * tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (added) * tests/regression/WorldTime/testsuite-worldtime.at (added) * tests/regression/testsuite.at (modified) Added single action to step backward and forward through time. - ... Fri, 09 Sep 2016 17:10:10 GMT Frederik Heber [73a5f7] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (added) * src/Actions/FragmentationAction/ParseFragmentResultsAction.def (added) * src/Actions/FragmentationAction/ParseFragmentResultsAction.hpp (added) * src/Actions/FragmentationAction/SaveFragmentResultsAction.cpp (added) * src/Actions/FragmentationAction/SaveFragmentResultsAction.def (added) * src/Actions/FragmentationAction/SaveFragmentResultsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/ParseSaveFragmentResults/post/results_empty.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/pre/create_results_dat.py (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/pre/results.dat (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added parsing and saving of fragment results container state. - ... Wed, 18 May 2016 22:02:53 GMT Frederik Heber [d8ed62] * doc/userguide/userguide.xml (modified) * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPartialChargesAction.def (modified) * tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at (modified) Rewrote FitPartialChargesAction to fit charges to currently selected ... Wed, 18 May 2016 22:02:06 GMT Frederik Heber [3004d2] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) FragmentationAction clears and inserts fragments into AtomFragments. Wed, 18 May 2016 22:02:06 GMT Frederik Heber [78202b] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/ParseAtomFragmentsAction.cpp (added) * src/Actions/PotentialAction/ParseAtomFragmentsAction.def (added) * src/Actions/PotentialAction/ParseAtomFragmentsAction.hpp (added) * src/Actions/PotentialAction/SaveAtomFragmentsAction.cpp (added) * src/Actions/PotentialAction/SaveAtomFragmentsAction.def (added) * src/Actions/PotentialAction/SaveAtomFragmentsAction.hpp (added) * src/Fragmentation/Homology/AtomFragmentsMap.hpp (modified) * src/Fragmentation/KeySet.hpp (modified) * tests/Python/AllActions/options.dat (modified) Adding potential action to parse and save atom fragment associations. ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [2082637] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/ParseParticleParametersAction.cpp (added) * src/Actions/PotentialAction/ParseParticleParametersAction.def (added) * src/Actions/PotentialAction/ParseParticleParametersAction.hpp (added) * src/Actions/PotentialAction/SaveParticleParametersAction.cpp (added) * src/Actions/PotentialAction/SaveParticleParametersAction.def (added) * src/Actions/PotentialAction/SaveParticleParametersAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/SaveParseParticleParameters/pre/harmonic.particles (added) * tests/regression/Potential/SaveParseParticleParameters/testsuite-potential-save-parse-particle-parameters.at (added) * tests/regression/Potential/testsuite-potential.at (modified) Added Parse- and SaveParticleParametersAction to parse/save ... Sun, 28 Feb 2016 17:59:42 GMT Frederik Heber [50d49d] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitPartialChargesAction.cpp (moved) * src/Actions/PotentialAction/FitPartialChargesAction.def (moved) * src/Actions/PotentialAction/FitPartialChargesAction.hpp (moved) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Potential/FitParticleCharges/testsuite-potential-fit-partial-charges.at (moved) * tests/GuiChecks/Potential/testsuite-potential.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/FitPartialCharges/pre/homology_grid.dat (moved) * tests/regression/Potential/FitPartialCharges/pre/water.pdb (moved) * tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at (moved) * tests/regression/Potential/testsuite-potential.at (modified) FIX: Renamed FitParticleCharges -> FitPartialCharges. - fitting ... Tue, 09 Feb 2016 07:11:35 GMT Frederik Heber [b40690] * doc/userguide/userguide.xml (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/PotentialTrainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) Fit..PotentialAction now allow setting maximum number of optimization ... Thu, 23 Jul 2015 22:34:39 GMT Frederik Heber [d12d818] * doc/userguide/userguide.xml (modified) DOCU: Corrected userguide. - this still needs some more work, e.g. ... Thu, 11 Jun 2015 23:21:40 GMT Frederik Heber [f3db60] * doc/userguide/userguide.xml (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/CommandAction/DryRunAction.cpp (added) * src/Actions/CommandAction/DryRunAction.def (added) * src/Actions/CommandAction/DryRunAction.hpp (added) * src/Actions/CommandAction/NoDryRunAction.cpp (added) * src/Actions/CommandAction/NoDryRunAction.def (added) * src/Actions/CommandAction/NoDryRunAction.hpp (added) * src/Actions/DryRunAdvocate.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/DryRun/post/session.py (added) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (added) * tests/regression/Options/DryRun/testsuite-options-dryrun.at (added) * tests/regression/Options/DryRun/testsuite-options-no-dryrun.at (added) * tests/regression/Options/testsuite-options.at (modified) Added DryRun and NoDryRun actions. - actions (un)set a flag inside ... Fri, 13 Feb 2015 09:18:04 GMT Frederik Heber [88afc9] * doc/userguide/userguide.xml (modified) * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondAddAction.def (modified) * src/Actions/BondAction/BondRemoveAction.cpp (modified) * src/Actions/BondAction/BondRemoveAction.def (modified) * tests/regression/Bond/Add/post/test_multiple.pdb (added) * tests/regression/Bond/Add/pre/test_multiple.pdb (added) * tests/regression/Bond/Add/testsuite-bond-add.at (modified) * tests/regression/Bond/Add/testsuite-bond-add_multiple.at (added) * tests/regression/Bond/Remove/post/test_multiple.pdb (added) * tests/regression/Bond/Remove/post/test_multiple_undo.pdb (added) * tests/regression/Bond/Remove/pre/test_multiple.pdb (added) * tests/regression/Bond/Remove/pre/test_multiple_undo.pdb (added) * tests/regression/Bond/Remove/testsuite-bond-remove.at (modified) * tests/regression/Bond/Remove/testsuite-bond-remove_multiple.at (added) * tests/regression/Bond/testsuite-bond.at (modified) * tests/regression/Makefile.am (modified) Enhanced add-bonds and remove-bonds to multiply selected pairs of ... Fri, 13 Feb 2015 09:17:52 GMT Frederik Heber [2fcef3] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/SaturateAction.cpp (added) * src/Actions/AtomAction/SaturateAction.def (added) * src/Actions/AtomAction/SaturateAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Atoms/Saturate/post/carbon.xyz (added) * tests/regression/Atoms/Saturate/post/nitrogen.xyz (added) * tests/regression/Atoms/Saturate/post/saturated_carbon.xyz (added) * tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz (added) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at (added) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added SaturateAction that uses SphericalPointDistribution. - added ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [066442] * doc/userguide/userguide.xml (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/AtomAction/TranslateAction.def (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (added) * src/Actions/MoleculeAction/TranslateAction.def (added) * src/Actions/MoleculeAction/TranslateAction.hpp (added) * tests/regression/Atoms/Translation/testsuite-atoms-translation.at (modified) * tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified) * tests/regression/Molecules/Translation/testsuite-molecules-translation.at (modified) * tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-load-multiply.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load-multiply.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load-multiply.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load-multiply.at (modified) Added TranslateMolecule action. - added translate-molecule to ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [a84e8d] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.cpp (added) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.def (added) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.hpp (added) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.cpp (added) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.def (added) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/box.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/empty.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/id2_4_missing.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/water_id2_4.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/pre/box.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/testsuite-selection-pop-molecule-selection.at (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/box.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/empty.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/id2_4_missing.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/water_id2_4.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/pre/box.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/testsuite-selection-push-molecule-selection.at (added) * tests/regression/Selection/Molecules/testsuite-selection-molecules.at (modified) Added Push/PopMolecules selection action. - added push-molecule to ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [3213f2] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp (added) * src/Actions/SelectionAction/Atoms/PopAtomsAction.def (added) * src/Actions/SelectionAction/Atoms/PopAtomsAction.hpp (added) * src/Actions/SelectionAction/Atoms/PushAtomsAction.cpp (added) * src/Actions/SelectionAction/Atoms/PushAtomsAction.def (added) * src/Actions/SelectionAction/Atoms/PushAtomsAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/PopAtomSelection/post/empty.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id01_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id01_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id0_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id0_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id1_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id1_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id2_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id2_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id3_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id3_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id4_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id4_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id5_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id5_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id6_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id6_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id7_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id7_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/test-undo.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/pre/test.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/testsuite-selection-pop-atom-selection.at (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/empty.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id01_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id01_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id0_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id0_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id1_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id1_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id2_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id2_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id3_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id3_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id4_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id4_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id5_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id5_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id6_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id6_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id7_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id7_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/test-undo.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/pre/test.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/testsuite-selection-push-atom-selection.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added Push/PopAtom selection actions. - added push-atom to ... Mon, 12 Jan 2015 22:10:30 GMT Frederik Heber [867473] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/RemoveAction.cpp (added) * src/Actions/MoleculeAction/RemoveAction.def (added) * src/Actions/MoleculeAction/RemoveAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/Remove/post/id0_2_missing.pdb (added) * tests/regression/Molecules/Remove/post/water_box.pdb (added) * tests/regression/Molecules/Remove/pre/water_box.pdb (added) * tests/regression/Molecules/Remove/testsuite-molecules-remove.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added new RemoveAction for molecules. - also add regression test. ... Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [8544b32] * doc/userguide/userguide.xml (modified) * src/documentation/constructs/tesselation.dox (modified) DOCU: Added extensive explanation how convexization works. - ... Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [cead3f] * doc/userguide/userguide.xml (modified) * utils/developer/raster3d/header.r3d (added) FIX: Raster3D needs header.r3d, which had been missing so far. Sun, 19 Oct 2014 17:12:11 GMT Frederik Heber [5c8807] * doc/userguide/userguide.xml (modified) * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.def (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.hpp (added) * src/Actions/AtomAction/TranslateToOriginAction.cpp (added) * src/Actions/AtomAction/TranslateToOriginAction.def (added) * src/Actions/AtomAction/TranslateToOriginAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted-weighted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/pre/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9 ... Sun, 19 Oct 2014 17:09:30 GMT Frederik Heber [9e1bfb] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.hpp (added) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (added) * src/Actions/PotentialAction/ParsePotentialsAction.def (added) * src/Actions/PotentialAction/ParsePotentialsAction.hpp (added) * src/Actions/PotentialAction/SavePotentialsAction.cpp (added) * src/Actions/PotentialAction/SavePotentialsAction.def (added) * src/Actions/PotentialAction/SavePotentialsAction.hpp (added) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialTrainer.cpp (added) * src/Potentials/PotentialTrainer.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9 Sun, 19 Oct 2014 17:08:51 GMT Frederik Heber [0ea063] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Actions/PotentialAction/SavePotentialsAction.cpp (added) * src/Actions/PotentialAction/SavePotentialsAction.def (added) * src/Actions/PotentialAction/SavePotentialsAction.hpp (added) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/PotentialTrainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Extracted SavePotentialsAction. - PotentialTrainer::StorePotentials ... Sun, 19 Oct 2014 17:08:50 GMT Frederik Heber [f1eabd] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (added) * src/Actions/PotentialAction/ParsePotentialsAction.def (added) * src/Actions/PotentialAction/ParsePotentialsAction.hpp (added) * tests/Python/AllActions/options.dat (modified) Extracted ParsePotentialsAction from FitCompoundPotentialAction. Sun, 19 Oct 2014 17:08:36 GMT Frederik Heber [98d166] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.hpp (added) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialTrainer.cpp (added) * src/Potentials/PotentialTrainer.hpp (added) Split FitPotentialAction into two actions. - FitPotentialAction ... Thu, 18 Sep 2014 23:32:23 GMT Frederik Heber [bbf6dc] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/MirrorAction.cpp (added) * src/Actions/AtomAction/MirrorAction.def (added) * src/Actions/AtomAction/MirrorAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Atoms/Mirror/post/test-mirrored.xyz (added) * tests/regression/Atoms/Mirror/post/test.xyz (added) * tests/regression/Atoms/Mirror/pre/test.xyz (added) * tests/regression/Atoms/Mirror/testsuite-atoms-mirror.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added AtomMirrorAction. - also added regression tests. Thu, 18 Sep 2014 17:23:14 GMT Frederik Heber [c7fe90] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/TranslateToOriginAction.cpp (added) * src/Actions/AtomAction/TranslateToOriginAction.def (added) * src/Actions/AtomAction/TranslateToOriginAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted-weighted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/pre/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added TranslateToOriginAction. - also added regression test. Thu, 18 Sep 2014 17:19:38 GMT Frederik Heber [f4b626a] * doc/userguide/userguide.xml (modified) * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.def (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) Added AverageMoleculeForceAction for measuring average force acting ... Wed, 17 Sep 2014 21:30:38 GMT Frederik Heber [9bce96] * doc/userguide/userguide.xml (modified) DOCU: Fixed all missing links in userguide. - each section now has ... Wed, 17 Sep 2014 21:29:44 GMT Frederik Heber [f73e06] * doc/userguide/userguide.xml (modified) * tests/CodeChecks/testsuite-action_present_in_userguide.at (modified) DOCU: Added all missing Actions to userguide. - removed XFAIL from ... Mon, 26 May 2014 09:15:08 GMT Frederik Heber [6029a6] * configure.ac (modified) * doc/Makefile.am (modified) * doc/userguide.xml (deleted) * doc/userguide/Makefile.am (added) * doc/userguide/catalog.xml.in (added) * doc/userguide/createguide.sh (added) * doc/userguide/css/html.css (added) * doc/userguide/pictures/dialog_add-atom_tooltip.png (added) * doc/userguide/pictures/dialog_box.png (added) * doc/userguide/pictures/dialog_complex.png (added) * doc/userguide/pictures/dialog_exit.png (added) * doc/userguide/pictures/example_basic_view.png (added) * doc/userguide/pictures/molecuilder_logo.png (moved) * doc/userguide/userguide.xml (added) * m4/ax_check_docbook.m4 (added) * src/documentation/mainpage.dox (modified) * src/documentation/userguide.dox (added) Added largely extended userguide with some images into subfolder of ...